GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DnaJ_CXXCXGXG - DnaJ central domain
Pfam: PF00684 (v26) Consensus Sequence
Length: 66
Sequences: 2394
Seq/Len: 36.27
HH_delta: 0.014 (11Mar13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
3_K61_K1.752153.938
26_Q41_Q1.600223.597
20_T46_K1.346053.026
28_V39_Q1.302042.927
16_K56_K1.215042.731
30_V37_V1.084382.437
10_K57_D1.029362.314
27_V45_P0.934862.101
10_K60_K0.921752.072
19_P46_K0.800561.799
28_V41_Q0.760251.709
37_V40_Q0.745661.676
29_Q42_Q0.712381.601
59_C62_C0.66141.487
2_P61_K0.629691.415
20_T45_P0.620671.395
15_P52_K0.554951.247
9_A13_K0.538591.211
20_T27_V0.528031.187
19_P53_I0.521641.173
17_T52_K0.518571.166
60_K63_K0.512871.153
46_K53_I0.500621.125
3_K10_K0.491461.105
1_C4_C0.460151.034
46_K61_K0.450241.012
18_C44_C0.440970.991
1_C59_C0.414840.932
11_P57_D0.40790.917
30_V40_Q0.406470.914
9_A15_P0.392990.883
17_T22_N0.38930.875
18_C21_C0.386950.870
31_Q37_V0.380180.855
3_K11_P0.377580.849
13_K57_D0.374960.843
30_V39_Q0.368810.829
31_Q38_F0.368190.828
31_Q40_Q0.366210.823
44_C49_G0.365630.822
30_V38_F0.361920.814
26_Q43_T0.354790.797
1_C62_C0.353490.795
4_C59_C0.346020.778
24_S28_V0.345640.777
29_Q40_Q0.341710.768
44_C47_C0.341630.768
10_K13_K0.338230.760
7_T11_P0.329420.740
4_C62_C0.32670.734
3_K20_T0.322390.725
9_A54_I0.321560.723
16_K46_K0.312590.703
15_P57_D0.308390.693
43_T48_G0.302270.679
12_G15_P0.301920.679
16_K53_I0.296960.668
58_P66_G0.296790.667
18_C23_G0.292770.658
26_Q37_V0.285360.641
37_V41_Q0.280890.631
24_S27_V0.278730.627
18_C49_G0.277410.624
5_H31_Q0.276730.622
21_C44_C0.273320.614
30_V42_Q0.267450.601
50_T53_I0.264450.594
14_K57_D0.263340.592
11_P14_K0.261390.588
21_C47_C0.256050.576
9_A58_P0.255180.574
8_G64_G0.249940.562
59_C64_G0.24670.555
36_G66_G0.246150.553
26_Q29_Q0.244110.549
24_S42_Q0.242190.544
22_N48_G0.238930.537
19_P56_K0.238730.537
2_P5_H0.23770.534
24_S30_V0.2310.519
45_P48_G0.230980.519
22_N65_S0.230830.519
16_K19_P0.230760.519
4_C64_G0.229090.515
54_I58_P0.227450.511
4_C21_C0.227220.511
4_C44_C0.226560.509
15_P54_I0.225940.508
8_G65_S0.217560.489
31_Q39_Q0.215520.484
24_S45_P0.212420.477
50_T65_S0.209470.471
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
1nltA0.984899.20.014
2cttA0.9242990.076
1exkA0.924298.90.142
3lczA0.596.90.512
1exkA0.757696.80.522
3pmqA196.70.528
2bx9A0.594.90.6
2bx9A0.606194.70.604
1nltA0.848594.20.614
3lczA0.606191.20.65

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